GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Marinobacter adhaerens HP15

Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate GFF2263 HP15_2213 3-ketoacyl-(acyl-carrier-protein) reductase

Query= uniprot:Q8EGC1
         (252 letters)



>FitnessBrowser__Marino:GFF2263
          Length = 247

 Score =  135 bits (339), Expect = 1e-36
 Identities = 86/254 (33%), Positives = 133/254 (52%), Gaps = 14/254 (5%)

Query: 1   MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSST-EVQGYA 59
           M L+ K  ++TG   G+G A+A   A  GA++      +   E    DL S+  +  G  
Sbjct: 1   MSLEGKTALVTGATRGIGQAIARALAAQGAEVVGTATSEAGAESITNDLQSAGYKGYGMV 60

Query: 60  LDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVIN 119
           +++ D   + AG   + E  G   +LVNNAGI RD +L++ KD         D + SV+ 
Sbjct: 61  MNVADPASIEAGLKELTEKSGAPLILVNNAGITRDNLLMRLKD---------DDWASVLE 111

Query: 120 VNLTGTFLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWAK 178
            NL+  +   +     M ++ + G I+NISS+ A  GN GQ NY A+KAGV   +   AK
Sbjct: 112 TNLSSVYRTSKAVLRGMAKA-KWGRIINISSVVAGMGNAGQGNYCAAKAGVEGFTRSLAK 170

Query: 179 ELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEN-- 236
           E++   I +  VAPG I T+MT  +  +    + +++P GRLG  EE+A+ V F+  +  
Sbjct: 171 EMSNRGITANCVAPGFIDTDMTKKLDDKQRGAMLEIIPAGRLGEPEEVAAVVAFLASDAA 230

Query: 237 DYVNGRVFEVDGGI 250
            YV G    V+GG+
Sbjct: 231 GYVTGETINVNGGM 244


Lambda     K      H
   0.317    0.134    0.369 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 179
Number of extensions: 15
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 252
Length of database: 247
Length adjustment: 24
Effective length of query: 228
Effective length of database: 223
Effective search space:    50844
Effective search space used:    50844
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory